org.jmol.jvxl.readers
Class ApbsReader

java.lang.Object
  extended by org.jmol.jvxl.readers.VoxelReader
      extended by org.jmol.jvxl.readers.VolumeFileReader
          extended by org.jmol.jvxl.readers.ApbsReader
All Implemented Interfaces:
VertexDataServer

 class ApbsReader
extends VolumeFileReader


Field Summary
 
Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
atomCount, br, canDownsample, endOfData, isAngstroms, line, negativeAtomCount, next
 
Fields inherited from class org.jmol.jvxl.readers.VoxelReader
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData
 
Constructor Summary
ApbsReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
protected  void readAtomCountAndOrigin()
           
protected  void readTitleLines()
           
protected  void readVoxelVector(int voxelVectorIndex)
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
determineFileType, discardTempData, getNextVoxelValue, getTokens, gotoData, nextVoxel, parseFloat, parseFloat, parseFloatNext, parseInt, parseInt, parseInt, parseIntNext, readExtraLine, readVolumeData, readVolumeParameters, readVolumetricHeader, readVoxelData, skipComments
 
Methods inherited from class org.jmol.jvxl.readers.VoxelReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, gotoAndReadVoxelData, initializeVolumetricData, isInside, jvxlUpdateInfo, readColorData, readSurfacePoint, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ApbsReader

ApbsReader(SurfaceGenerator sg,
           java.io.BufferedReader br)
Method Detail

readTitleLines

protected void readTitleLines()
                       throws java.lang.Exception
Overrides:
readTitleLines in class VolumeFileReader
Throws:
java.lang.Exception

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()
                               throws java.lang.Exception
Overrides:
readAtomCountAndOrigin in class VolumeFileReader
Throws:
java.lang.Exception

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)
                        throws java.lang.Exception
Overrides:
readVoxelVector in class VolumeFileReader
Throws:
java.lang.Exception